Starting phenix.real_space_refine
on Sat Aug 23 00:39:53 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9c91_45359/08_2025/9c91_45359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c91_45359/08_2025/9c91_45359.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c91_45359/08_2025/9c91_45359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c91_45359/08_2025/9c91_45359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c91_45359/08_2025/9c91_45359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c91_45359/08_2025/9c91_45359.cif"
  }
  resolution = 2.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.054
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     K       1      8.98       5
     Fe      5      7.16       5
     P       4      5.49       5
     S      31      5.16       5
     C    5532      2.51       5
     N    1545      2.21       5
     O    1666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8784
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4119
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 518, 4093
          Classifications: {'peptide': 518}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 496}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 518, 4093
          Classifications: {'peptide': 518}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 496}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4146
    Chain: "B"
      Number of atoms: 4504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4504
          Classifications: {'peptide': 570}
          Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 542}
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 84
          Unusual residues: {'FAD': 1, 'FMN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 77
          Unusual residues: {'  K': 1, 'PO4': 1, 'SF4': 1, 'SRM': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unsupported chir.volume_sign: {'cros': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7575  SG  CYS B 434      31.093  38.242  41.422  1.00 35.39           S
  ATOM   7619  SG  CYS B 440      30.295  43.097  45.770  1.00 39.39           S
  ATOM   7919  SG  CYS B 479      25.725  42.645  42.397  1.00 45.34           S
  ATOM   7944  SG  CYS B 483      31.365  44.001  39.596  1.00 61.15           S
  ATOM   7944  SG  CYS B 483      31.365  44.001  39.596  1.00 61.15           S

  Time building chain proxies: 2.66, per 1000 atoms: 0.30
  Number of scatterers: 8784
  At special positions: 0
  Unit cell: (77.265, 86.445, 139.995, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      5     26.01
     K       1     19.00
     S      31     16.00
     P       4     15.00
     O    1666      8.00
     N    1545      7.00
     C    5532      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 316.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 B 603 "
        pdb="FE4  SF4 B 603 " - pdb=" SG  CYS B 483 "
        pdb="FE2  SF4 B 603 " - pdb=" SG  CYS B 440 "
        pdb="FE1  SF4 B 603 " - pdb=" SG  CYS B 434 "
        pdb="FE3  SF4 B 603 " - pdb=" SG  CYS B 479 "
      Number of angles added : 12


  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2022

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 10 sheets defined
      42.5% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 90
      removed outlier: 3.638A  pdb=" N   VAL A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 109
      removed outlier: 5.357A  pdb=" N   ALA A 107 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 136
    Processing helix  chain 'A' and resid 162 through 175
    Processing helix  chain 'A' and resid 190 through 204
      removed outlier: 3.626A  pdb=" N   ALA A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ARG A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 267
      removed outlier: 4.358A  pdb=" N   GLY A 267 " --> pdb=" O   GLY A 264 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 264 through 267'
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 311 through 318
    Processing helix  chain 'A' and resid 325 through 335
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'A' and resid 347 through 358
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 372 through 380
    Processing helix  chain 'A' and resid 393 through 398
    Processing helix  chain 'A' and resid 419 through 427
      removed outlier: 3.575A  pdb=" N   SER A 423 " --> pdb=" O   GLY A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 463
      removed outlier: 3.578A  pdb=" N   GLY A 463 " --> pdb=" O   PRO A 460 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 460 through 463'
    Processing helix  chain 'A' and resid 464 through 478
    Processing helix  chain 'A' and resid 491 through 496
      removed outlier: 3.814A  pdb=" N   PHE A 496 " --> pdb=" O   PHE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 508
    Processing helix  chain 'A' and resid 527 through 535
      removed outlier: 3.568A  pdb=" N   LYS A 531 " --> pdb=" O   TYR A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 545
    Processing helix  chain 'A' and resid 557 through 574
    Processing helix  chain 'A' and resid 577 through 591
    Processing helix  chain 'B' and resid 16 through 25
    Processing helix  chain 'B' and resid 31 through 36
    Processing helix  chain 'B' and resid 47 through 55
      removed outlier: 4.854A  pdb=" N   ARG B  53 " --> pdb=" O   PHE B  49 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   PHE B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   HIS B  55 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 72
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 93 through 106
    Processing helix  chain 'B' and resid 126 through 128
      No H-bonds generated for 'chain 'B' and resid 126 through 128'
    Processing helix  chain 'B' and resid 129 through 140
      removed outlier: 3.807A  pdb=" N   HIS B 134 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 181
    Processing helix  chain 'B' and resid 186 through 192
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.517A  pdb=" N   ASN B 233 " --> pdb=" O   LEU B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 297
    Processing helix  chain 'B' and resid 306 through 315
    Processing helix  chain 'B' and resid 315 through 328
    Processing helix  chain 'B' and resid 362 through 364
      No H-bonds generated for 'chain 'B' and resid 362 through 364'
    Processing helix  chain 'B' and resid 375 through 386
    Processing helix  chain 'B' and resid 404 through 418
      removed outlier: 4.245A  pdb=" N   ALA B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   LYS B 410 " --> pdb=" O   SER B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 430
      removed outlier: 3.504A  pdb=" N   GLU B 429 " --> pdb=" O   THR B 425 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASN B 430 " --> pdb=" O   PRO B 426 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 425 through 430'
    Processing helix  chain 'B' and resid 450 through 465
    Processing helix  chain 'B' and resid 485 through 489
      removed outlier: 3.690A  pdb=" N   ALA B 489 " --> pdb=" O   ALA B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 542
      removed outlier: 3.791A  pdb=" N   LYS B 540 " --> pdb=" O   GLY B 536 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG B 542 " --> pdb=" O   TRP B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 555
    Processing helix  chain 'B' and resid 563 through 568
      removed outlier: 3.649A  pdb=" N   LEU B 568 " --> pdb=" O   PRO B 564 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97
      removed outlier: 6.888A  pdb=" N   LEU A 112 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   PHE A 151 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL A 114 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 8.723A  pdb=" N   VAL A 150 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ASP A 182 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   SER A 152 " --> pdb=" O   ASP A 182 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL A 184 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 279
      removed outlier: 4.460A  pdb=" N   ARG A 436 " --> pdb=" O   TRP A 279 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   LEU A 241 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ASP A 262 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   ASP A 255 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 304
    Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 412
    Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 518
      removed outlier: 6.339A  pdb=" N   ASN A 483 " --> pdb=" O   ARG A 513 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   ASP A 515 " --> pdb=" O   ASN A 483 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   LEU A 485 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ALA A 517 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   PHE A 487 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   ILE A 549 " --> pdb=" O   GLN A 595 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ASP A 597 " --> pdb=" O   ILE A 549 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL A 551 " --> pdb=" O   ASP A 597 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   TYR A 599 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   GLY A 553 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 60
      removed outlier: 6.670A  pdb=" N   LEU B  82 " --> pdb=" O   HIS B 123 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   HIS B 123 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92
      removed outlier: 3.846A  pdb=" N   ASP B 389 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY B 402 " --> pdb=" O   TRP B 356 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   TRP B 356 " --> pdb=" O   GLY B 402 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 156 through 157
      removed outlier: 6.335A  pdb=" N   LEU B 156 " --> pdb=" O   VAL B 220 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR B 219 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   ALA B 239 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL B 221 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   ALA B 241 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   GLU B 242 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   LEU B 246 " --> pdb=" O   GLU B 242 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   VAL B 247 " --> pdb=" O   PRO B 278 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   PHE B 249 " --> pdb=" O   TYR B 276 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   TYR B 276 " --> pdb=" O   PHE B 249 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU B 251 " --> pdb=" O   PHE B 274 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 370
    Processing sheet with id=AB1, first strand: chain 'B' and resid 431 through 433
      removed outlier: 6.696A  pdb=" N   MET B 432 " --> pdb=" O   VAL B 476 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ARG B 500 " --> pdb=" O   LYS B 496 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   TYR B 501 " --> pdb=" O   ASN B 521 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   LEU B 505 " --> pdb=" O   MET B 517 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   MET B 517 " --> pdb=" O   LEU B 505 " (cutoff:3.500A)

    355 hydrogen bonds defined for protein.
    1006 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 1.03 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.43: 3816
        1.43 -     1.64: 5102
        1.64 -     1.86: 46
        1.86 -     2.07: 4
        2.07 -     2.28: 12
  Bond restraints: 8980
  Sorted by residual:
  bond pdb=" C4  FMN A 601 "
       pdb=" C4A FMN A 601 "
    ideal  model  delta    sigma   weight residual
    1.485  1.396  0.089 2.00e-02 2.50e+03 2.00e+01
  bond pdb=" O3P FAD A 600 "
       pdb=" P   FAD A 600 "
    ideal  model  delta    sigma   weight residual
    1.660  1.578  0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" C4A FMN A 601 "
       pdb=" N5  FMN A 601 "
    ideal  model  delta    sigma   weight residual
    1.300  1.379 -0.079 2.00e-02 2.50e+03 1.55e+01
  bond pdb=" O5B FAD A 600 "
       pdb=" PA  FAD A 600 "
    ideal  model  delta    sigma   weight residual
    1.634  1.567  0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" O5' FAD A 600 "
       pdb=" P   FAD A 600 "
    ideal  model  delta    sigma   weight residual
    1.637  1.571  0.066 2.00e-02 2.50e+03 1.08e+01
  ... (remaining 8975 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 11936
        1.91 -     3.81: 197
        3.81 -     5.72: 48
        5.72 -     7.63: 19
        7.63 -     9.53: 7
  Bond angle restraints: 12207
  Sorted by residual:
  angle pdb=" C   SER B 436 "
        pdb=" CA  SER B 436 "
        pdb=" CB  SER B 436 "
      ideal   model   delta    sigma   weight residual
     116.54  110.42    6.12 1.15e+00 7.56e-01 2.83e+01
  angle pdb=" C   LYS A  90 "
        pdb=" N   LEU A  91 "
        pdb=" CA  LEU A  91 "
      ideal   model   delta    sigma   weight residual
     121.54  129.37   -7.83 1.91e+00 2.74e-01 1.68e+01
  angle pdb=" CA  SER B 436 "
        pdb=" C   SER B 436 "
        pdb=" N   PHE B 437 "
      ideal   model   delta    sigma   weight residual
     119.52  116.86    2.66 7.90e-01 1.60e+00 1.13e+01
  angle pdb=" CA  GLU A 330 "
        pdb=" CB  GLU A 330 "
        pdb=" CG  GLU A 330 "
      ideal   model   delta    sigma   weight residual
     114.10  120.55   -6.45 2.00e+00 2.50e-01 1.04e+01
  angle pdb=" C2B SRM B 604 "
        pdb=" C3B SRM B 604 "
        pdb=" C4B SRM B 604 "
      ideal   model   delta    sigma   weight residual
     108.00   98.47    9.53 3.00e+00 1.11e-01 1.01e+01
  ... (remaining 12202 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.18: 4997
       28.18 -    56.36: 363
       56.36 -    84.53: 35
       84.53 -   112.71: 2
      112.71 -   140.89: 1
  Dihedral angle restraints: 5398
    sinusoidal: 2253
      harmonic: 3145
  Sorted by residual:
  dihedral pdb=" C3B SRM B 604 "
           pdb=" C2B SRM B 604 "
           pdb=" CDB SRM B 604 "
           pdb=" CEB SRM B 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -54.26   86.63 -140.89     1      2.00e+01 2.50e-03 4.26e+01
  dihedral pdb=" CA  ASN B 149 "
           pdb=" C   ASN B 149 "
           pdb=" N   ASP B 150 "
           pdb=" CA  ASP B 150 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.53  -16.47     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ASP B 202 "
           pdb=" CB  ASP B 202 "
           pdb=" CG  ASP B 202 "
           pdb=" OD1 ASP B 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.61   56.61     1      2.00e+01 2.50e-03 1.08e+01
  ... (remaining 5395 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 855
       0.035 -    0.070: 325
       0.070 -    0.105: 103
       0.105 -    0.140: 38
       0.140 -    0.175: 4
  Chirality restraints: 1325
  Sorted by residual:
  chirality pdb=" CB  ILE B 206 "
            pdb=" CA  ILE B 206 "
            pdb=" CG1 ILE B 206 "
            pdb=" CG2 ILE B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CB  THR A 162 "
            pdb=" CA  THR A 162 "
            pdb=" OG1 THR A 162 "
            pdb=" CG2 THR A 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.16 2.00e-01 2.50e+01 6.77e-01
  chirality pdb=" C2A SRM B 604 "
            pdb=" C1A SRM B 604 "
            pdb=" CDA SRM B 604 "
            pdb=" CMA SRM B 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63    2.48    0.15 2.00e-01 2.50e+01 5.59e-01
  ... (remaining 1322 not shown)

  Planarity restraints: 1590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 335 "    0.034 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO B 336 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO B 336 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 336 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  SRM B 604 "   -0.002 2.00e-02 2.50e+03   1.51e-02 2.84e+00
        pdb=" C1B SRM B 604 "   -0.011 2.00e-02 2.50e+03
        pdb=" C2B SRM B 604 "    0.015 2.00e-02 2.50e+03
        pdb=" C4A SRM B 604 "    0.019 2.00e-02 2.50e+03
        pdb=" CHB SRM B 604 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 131 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO B 132 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 132 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 132 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1587 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.78: 1956
        2.78 -     3.37: 9633
        3.37 -     3.96: 17728
        3.96 -     4.55: 25236
        4.55 -     5.14: 37320
  Nonbonded interactions: 91873
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 270 "
            pdb=" O   GLU A 400 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   GLU B 287 "
            pdb=" OG1 THR B 291 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   GLU A 109 "
            pdb=" OG1 THR A 146 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER A 252 "
            pdb=" OD1 ASP A 495 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   GLY A 463 "
            pdb=" OG  SER A 552 "
     model   vdw
     2.256 3.040
  ... (remaining 91868 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.18 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.800
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0042
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   8987  Z= 0.210
  Angle     :  0.757  19.584  12219  Z= 0.321
  Chirality :  0.043   0.175   1325
  Planarity :  0.004   0.051   1590
  Dihedral  : 18.115 140.888   3376
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.51 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 27.80 %
    Favored  : 69.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.26), residues: 1086
  helix:  1.40 (0.28), residues: 389
  sheet: -0.34 (0.37), residues: 203
  loop : -0.46 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  29 
 TYR   0.019   0.001   TYR A 332 
 PHE   0.016   0.002   PHE A 103 
 TRP   0.015   0.001   TRP A 295 
 HIS   0.002   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8980)
  covalent geometry    : angle       0.69069 (12207)
  hydrogen bonds       : bond        0.16652 (  355)
  hydrogen bonds       : angle       6.99197 ( 1006)
  metal coordination   : bond        0.01592 (    4)
  metal coordination   : angle       9.90915 (   12)
  Misc. bond           : bond        0.02842 (    3)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  543 ILE cc_start: -0.0194 (mt) cc_final: -0.1597 (mm)
REVERT: A  592 ARG cc_start: 0.0616 (mmm160) cc_final: -0.1205 (ttm170)
REVERT: B  135 GLN cc_start: 0.0618 (mm110) cc_final: -0.0438 (pt0)
REVERT: B  136 MET cc_start: 0.2872 (pp-130) cc_final: 0.1155 (mmm)
REVERT: B  192 TRP cc_start: 0.0643 (m100) cc_final: 0.0288 (m100)
REVERT: B  439 THR cc_start: -0.0495 (OUTLIER) cc_final: -0.0715 (p)
  outliers start: 24
  outliers final: 5
  residues processed: 86
  average time/residue: 0.4215
  time to fit residues: 39.9590
Evaluate side-chains
  52 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  439 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   40.0000
   chunk 100 optimal weight:    0.0000
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.1846

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5016 r_free = 0.5016 target = 0.293949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.261114 restraints weight = 26292.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.4763 rms_B_bonded: 6.64
r_work (final): 0.4763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4764
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4764 r_free = 0.4764    target_work(ls_wunit_k1) = 0.260         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4763 r_free = 0.4763    target_work(ls_wunit_k1) = 0.260         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0530
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8987  Z= 0.191
  Angle     :  0.849  18.922  12219  Z= 0.378
  Chirality :  0.046   0.185   1325
  Planarity :  0.006   0.048   1590
  Dihedral  :  7.561 139.101   1281
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.53 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 24.95 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.26), residues: 1086
  helix:  1.23 (0.27), residues: 392
  sheet: -0.36 (0.35), residues: 205
  loop : -0.63 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 596 
 TYR   0.019   0.002   TYR A 527 
 PHE   0.022   0.003   PHE B 122 
 TRP   0.023   0.002   TRP A 540 
 HIS   0.009   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8980)
  covalent geometry    : angle       0.76945 (12207)
  hydrogen bonds       : bond        0.04084 (  355)
  hydrogen bonds       : angle       5.62124 ( 1006)
  metal coordination   : bond        0.02464 (    4)
  metal coordination   : angle      11.47599 (   12)
  Misc. bond           : bond        0.01905 (    3)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 47
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.0489 (OUTLIER) cc_final: -0.0186 (mtpt)
REVERT: A  110 LYS cc_start: 0.2089 (mmtt) cc_final: 0.1516 (tppt)
REVERT: A  181 LEU cc_start: 0.1277 (tm) cc_final: 0.1034 (tt)
REVERT: A  582 ASP cc_start: 0.3722 (t0) cc_final: 0.3270 (t70)
REVERT: A  591 GLU cc_start: -0.0002 (OUTLIER) cc_final: -0.0556 (tp30)
REVERT: A  592 ARG cc_start: 0.1386 (mmm160) cc_final: -0.0952 (mtt90)
REVERT: B  136 MET cc_start: 0.3109 (OUTLIER) cc_final: 0.1397 (mmm)
REVERT: B  413 LYS cc_start: 0.2465 (OUTLIER) cc_final: 0.2036 (mmtt)
REVERT: B  485 ARG cc_start: 0.0070 (mtm-85) cc_final: -0.1376 (mtt180)
REVERT: B  487 MET cc_start: 0.3181 (mpp) cc_final: 0.2258 (mmt)
REVERT: B  533 GLU cc_start: 0.2525 (OUTLIER) cc_final: 0.2192 (tp30)
  outliers start: 47
  outliers final: 13
  residues processed: 89
  average time/residue: 0.4620
  time to fit residues: 44.7405
Evaluate side-chains
  61 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  458 ILE
Chi-restraints excluded: chain B residue  533 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 40 optimal weight:   10.0000
   chunk 77 optimal weight:   30.0000
   chunk 46 optimal weight:    2.9990
   chunk 67 optimal weight:   30.0000
   chunk 59 optimal weight:    0.9980
   chunk 107 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.3582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  59 GLN
B  78 HIS
** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 236 ASN
B 250 ASN
** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5016 r_free = 0.5016 target = 0.295553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.248843 restraints weight = 24466.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.4647 rms_B_bonded: 3.89
r_work (final): 0.4647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4649 r_free = 0.4649    target_work(ls_wunit_k1) = 0.248         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4649 r_free = 0.4649    target_work(ls_wunit_k1) = 0.248         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0781
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8987  Z= 0.187
  Angle     :  0.884  27.848  12219  Z= 0.391
  Chirality :  0.046   0.186   1325
  Planarity :  0.007   0.062   1590
  Dihedral  :  7.725 137.152   1274
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.99 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 25.16 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.26), residues: 1086
  helix:  0.89 (0.27), residues: 392
  sheet: -0.22 (0.39), residues: 182
  loop : -0.86 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 500 
 TYR   0.021   0.002   TYR B 211 
 PHE   0.026   0.002   PHE A 161 
 TRP   0.017   0.002   TRP A 484 
 HIS   0.004   0.001   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 8980)
  covalent geometry    : angle       0.80404 (12207)
  hydrogen bonds       : bond        0.04237 (  355)
  hydrogen bonds       : angle       5.60420 ( 1006)
  metal coordination   : bond        0.01402 (    4)
  metal coordination   : angle      11.71609 (   12)
  Misc. bond           : bond        0.03467 (    3)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 47
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.2306 (mmtt) cc_final: 0.1682 (tppt)
REVERT: A  168 PHE cc_start: 0.1317 (OUTLIER) cc_final: 0.0950 (m-80)
REVERT: A  379 LEU cc_start: 0.0926 (OUTLIER) cc_final: 0.0639 (mm)
REVERT: A  444 ASN cc_start: 0.1327 (OUTLIER) cc_final: -0.0159 (p0)
REVERT: A  532 LEU cc_start: 0.0613 (OUTLIER) cc_final: -0.0309 (mt)
REVERT: B  125 ILE cc_start: -0.2114 (OUTLIER) cc_final: -0.3383 (tp)
REVERT: B  136 MET cc_start: 0.3331 (OUTLIER) cc_final: 0.1410 (mmm)
REVERT: B  186 ARG cc_start: 0.1477 (mtt90) cc_final: 0.1163 (mmm160)
REVERT: B  192 TRP cc_start: 0.2194 (m100) cc_final: 0.1170 (m100)
REVERT: B  203 GLU cc_start: 0.2275 (OUTLIER) cc_final: 0.0200 (mt-10)
REVERT: B  413 LYS cc_start: 0.2761 (OUTLIER) cc_final: 0.2169 (mmtt)
REVERT: B  462 MET cc_start: 0.2951 (tpp) cc_final: -0.0171 (pmm)
  outliers start: 42
  outliers final: 20
  residues processed: 82
  average time/residue: 0.4598
  time to fit residues: 40.8572
Evaluate side-chains
  69 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 41
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 89 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 70 optimal weight:    0.5980
   chunk 100 optimal weight:    6.9990
   chunk 75 optimal weight:   10.0000
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 106 ASN
B 129 ASN
B 195 GLN
B 395 ASN
B 504 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5077 r_free = 0.5077 target = 0.302858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.254236 restraints weight = 27915.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.4688 rms_B_bonded: 4.41
r_work (final): 0.4688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4695 r_free = 0.4695    target_work(ls_wunit_k1) = 0.253         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4695 r_free = 0.4695    target_work(ls_wunit_k1) = 0.253         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0709
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8987  Z= 0.141
  Angle     :  0.791  27.358  12219  Z= 0.334
  Chirality :  0.044   0.173   1325
  Planarity :  0.005   0.058   1590
  Dihedral  :  7.500 143.466   1274
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.62 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 25.93 %
    Favored  : 70.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.26), residues: 1086
  helix:  1.05 (0.27), residues: 393
  sheet: -0.30 (0.38), residues: 182
  loop : -0.75 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 520 
 TYR   0.021   0.001   TYR B  27 
 PHE   0.020   0.002   PHE B  49 
 TRP   0.008   0.001   TRP A 484 
 HIS   0.006   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8980)
  covalent geometry    : angle       0.70099 (12207)
  hydrogen bonds       : bond        0.03486 (  355)
  hydrogen bonds       : angle       5.18666 ( 1006)
  metal coordination   : bond        0.01302 (    4)
  metal coordination   : angle      11.71783 (   12)
  Misc. bond           : bond        0.02502 (    3)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 45
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 GLU cc_start: -0.0124 (OUTLIER) cc_final: -0.0393 (tp30)
REVERT: A  379 LEU cc_start: 0.0926 (OUTLIER) cc_final: 0.0691 (mm)
REVERT: A  532 LEU cc_start: 0.0577 (OUTLIER) cc_final: -0.0342 (mt)
REVERT: A  582 ASP cc_start: 0.3196 (t0) cc_final: 0.2229 (t70)
REVERT: B   36 LEU cc_start: -0.0315 (OUTLIER) cc_final: -0.0648 (tp)
REVERT: B   37 ASN cc_start: 0.4155 (m-40) cc_final: 0.2786 (t0)
REVERT: B  125 ILE cc_start: -0.2722 (OUTLIER) cc_final: -0.3590 (mt)
REVERT: B  136 MET cc_start: 0.3478 (OUTLIER) cc_final: 0.1295 (mmm)
REVERT: B  192 TRP cc_start: 0.2038 (m100) cc_final: 0.1084 (m100)
REVERT: B  368 LEU cc_start: 0.0183 (OUTLIER) cc_final: -0.0665 (mp)
REVERT: B  413 LYS cc_start: 0.2732 (OUTLIER) cc_final: 0.2136 (mmtt)
REVERT: B  462 MET cc_start: 0.3111 (tpp) cc_final: -0.0087 (pmm)
REVERT: B  485 ARG cc_start: 0.1570 (mtm180) cc_final: 0.1187 (mtt180)
REVERT: B  487 MET cc_start: 0.1171 (mpp) cc_final: 0.0830 (mpp)
  outliers start: 34
  outliers final: 16
  residues processed: 71
  average time/residue: 0.4446
  time to fit residues: 34.8008
Evaluate side-chains
  63 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 39
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 67 optimal weight:   30.0000
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 105 optimal weight:   40.0000
   chunk 62 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5088 r_free = 0.5088 target = 0.304356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.257024 restraints weight = 28545.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.4700 rms_B_bonded: 4.47
r_work (final): 0.4700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4709 r_free = 0.4709    target_work(ls_wunit_k1) = 0.255         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4709 r_free = 0.4709    target_work(ls_wunit_k1) = 0.255         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0726
moved from start:          0.5047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8987  Z= 0.128
  Angle     :  0.756  24.505  12219  Z= 0.314
  Chirality :  0.042   0.164   1325
  Planarity :  0.005   0.056   1590
  Dihedral  :  7.309 140.773   1274
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.25 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 26.04 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.26), residues: 1086
  helix:  1.17 (0.27), residues: 395
  sheet: -0.48 (0.38), residues: 195
  loop : -0.72 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  77 
 TYR   0.016   0.001   TYR B  27 
 PHE   0.016   0.002   PHE A 161 
 TRP   0.007   0.001   TRP A 197 
 HIS   0.005   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8980)
  covalent geometry    : angle       0.66503 (12207)
  hydrogen bonds       : bond        0.03214 (  355)
  hydrogen bonds       : angle       5.01339 ( 1006)
  metal coordination   : bond        0.00863 (    4)
  metal coordination   : angle      11.48855 (   12)
  Misc. bond           : bond        0.01554 (    3)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 40
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 GLU cc_start: -0.0170 (OUTLIER) cc_final: -0.0634 (mm-30)
REVERT: A  379 LEU cc_start: 0.0937 (OUTLIER) cc_final: 0.0731 (mm)
REVERT: A  532 LEU cc_start: 0.0550 (OUTLIER) cc_final: -0.0360 (mt)
REVERT: B   36 LEU cc_start: -0.0064 (OUTLIER) cc_final: -0.0486 (tp)
REVERT: B  125 ILE cc_start: -0.2672 (OUTLIER) cc_final: -0.3557 (mt)
REVERT: B  136 MET cc_start: 0.3328 (OUTLIER) cc_final: 0.1410 (mmm)
REVERT: B  368 LEU cc_start: 0.0427 (OUTLIER) cc_final: -0.0353 (mp)
REVERT: B  375 LEU cc_start: -0.0398 (OUTLIER) cc_final: -0.1140 (mt)
REVERT: B  392 ILE cc_start: 0.1546 (mp) cc_final: 0.1237 (mp)
REVERT: B  413 LYS cc_start: 0.2558 (OUTLIER) cc_final: 0.2092 (mmtt)
REVERT: B  462 MET cc_start: 0.3180 (OUTLIER) cc_final: 0.0023 (pmm)
REVERT: B  487 MET cc_start: 0.1452 (mpp) cc_final: 0.1074 (mpp)
  outliers start: 36
  outliers final: 17
  residues processed: 66
  average time/residue: 0.3967
  time to fit residues: 28.8449
Evaluate side-chains
  64 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 37
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 86 optimal weight:    9.9990
   chunk 75 optimal weight:    0.7980
   chunk 104 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0040
   chunk 90 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.9394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 396 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5098 r_free = 0.5098 target = 0.305974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.235773 restraints weight = 23694.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.4458 rms_B_bonded: 6.63
r_work: 0.4240 rms_B_bonded: 5.35 restraints_weight: 2.0000
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4234 r_free = 0.4234    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4234 r_free = 0.4234    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0297
moved from start:          0.5436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8987  Z= 0.140
  Angle     :  0.772  22.893  12219  Z= 0.326
  Chirality :  0.043   0.158   1325
  Planarity :  0.005   0.057   1590
  Dihedral  :  7.273 138.474   1274
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.62 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 26.15 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.26), residues: 1086
  helix:  1.14 (0.27), residues: 395
  sheet: -0.45 (0.38), residues: 194
  loop : -0.72 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 186 
 TYR   0.023   0.001   TYR B  27 
 PHE   0.017   0.002   PHE A 487 
 TRP   0.007   0.001   TRP A 197 
 HIS   0.007   0.001   HIS B 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8980)
  covalent geometry    : angle       0.68988 (12207)
  hydrogen bonds       : bond        0.03346 (  355)
  hydrogen bonds       : angle       5.03232 ( 1006)
  metal coordination   : bond        0.00833 (    4)
  metal coordination   : angle      11.04697 (   12)
  Misc. bond           : bond        0.01575 (    3)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 42
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 GLU cc_start: 0.0282 (OUTLIER) cc_final: -0.0191 (tp30)
REVERT: A  444 ASN cc_start: 0.0518 (OUTLIER) cc_final: -0.1215 (p0)
REVERT: A  539 LEU cc_start: -0.0641 (OUTLIER) cc_final: -0.0930 (mt)
REVERT: B  125 ILE cc_start: -0.4728 (OUTLIER) cc_final: -0.5013 (tp)
REVERT: B  136 MET cc_start: 0.2810 (OUTLIER) cc_final: 0.0858 (mmm)
REVERT: B  368 LEU cc_start: -0.0375 (OUTLIER) cc_final: -0.0639 (mp)
REVERT: B  373 ARG cc_start: -0.1820 (OUTLIER) cc_final: -0.2952 (mmm-85)
REVERT: B  375 LEU cc_start: -0.1510 (OUTLIER) cc_final: -0.1893 (mt)
REVERT: B  413 LYS cc_start: 0.2790 (OUTLIER) cc_final: 0.2284 (mmtt)
REVERT: B  462 MET cc_start: 0.3090 (OUTLIER) cc_final: -0.0107 (pmm)
REVERT: B  487 MET cc_start: 0.1916 (mpp) cc_final: 0.1358 (mpp)
REVERT: B  533 GLU cc_start: 0.3000 (OUTLIER) cc_final: 0.2274 (tp30)
  outliers start: 42
  outliers final: 18
  residues processed: 74
  average time/residue: 0.4485
  time to fit residues: 36.4178
Evaluate side-chains
  69 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 40
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   57 MET
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  373 ARG
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  533 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 43 optimal weight:    8.9990
   chunk 46 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5116 r_free = 0.5116 target = 0.308593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4856 r_free = 0.4856 target = 0.272123 restraints weight = 20634.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.4830 rms_B_bonded: 5.21
r_work (final): 0.4830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4838 r_free = 0.4838    target_work(ls_wunit_k1) = 0.271         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4838 r_free = 0.4838    target_work(ls_wunit_k1) = 0.271         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1043
moved from start:          0.6451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8987  Z= 0.193
  Angle     :  0.888  24.623  12219  Z= 0.399
  Chirality :  0.048   0.343   1325
  Planarity :  0.006   0.058   1590
  Dihedral  :  7.755 137.377   1274
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.36 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 25.93 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.25), residues: 1086
  helix:  0.67 (0.27), residues: 397
  sheet: -0.16 (0.42), residues: 166
  loop : -1.08 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  77 
 TYR   0.023   0.002   TYR B  27 
 PHE   0.030   0.003   PHE A 161 
 TRP   0.012   0.001   TRP A 540 
 HIS   0.011   0.001   HIS B 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 8980)
  covalent geometry    : angle       0.81798 (12207)
  hydrogen bonds       : bond        0.04278 (  355)
  hydrogen bonds       : angle       5.42653 ( 1006)
  metal coordination   : bond        0.01490 (    4)
  metal coordination   : angle      11.03154 (   12)
  Misc. bond           : bond        0.03013 (    3)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 50
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.1184 (OUTLIER) cc_final: -0.1073 (p0)
REVERT: A  486 PHE cc_start: 0.0456 (OUTLIER) cc_final: -0.0145 (m-10)
REVERT: A  528 VAL cc_start: 0.0105 (OUTLIER) cc_final: -0.0341 (p)
REVERT: A  539 LEU cc_start: 0.0427 (OUTLIER) cc_final: -0.0264 (mt)
REVERT: B   19 GLU cc_start: 0.3052 (mm-30) cc_final: 0.2544 (tp30)
REVERT: B  125 ILE cc_start: -0.2247 (OUTLIER) cc_final: -0.2882 (mt)
REVERT: B  136 MET cc_start: 0.3837 (OUTLIER) cc_final: 0.1702 (mmm)
REVERT: B  368 LEU cc_start: 0.0811 (OUTLIER) cc_final: 0.0521 (mp)
REVERT: B  373 ARG cc_start: -0.0292 (OUTLIER) cc_final: -0.1739 (mtm-85)
REVERT: B  375 LEU cc_start: -0.0767 (OUTLIER) cc_final: -0.1352 (mt)
REVERT: B  413 LYS cc_start: 0.2867 (OUTLIER) cc_final: 0.2137 (mmtt)
REVERT: B  462 MET cc_start: 0.3209 (OUTLIER) cc_final: 0.0164 (pmm)
REVERT: B  487 MET cc_start: 0.1407 (mpp) cc_final: 0.0825 (mpp)
  outliers start: 40
  outliers final: 23
  residues processed: 77
  average time/residue: 0.4780
  time to fit residues: 40.0716
Evaluate side-chains
  77 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 43
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  373 ARG
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  462 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 97 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   chunk 38 optimal weight:   20.0000
   chunk 87 optimal weight:    0.9990
   chunk 94 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 180 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5133 r_free = 0.5133 target = 0.310127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.253071 restraints weight = 26659.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.4647 rms_B_bonded: 6.99
r_work: 0.4401 rms_B_bonded: 5.24 restraints_weight: 2.0000
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4399 r_free = 0.4399    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4398 r_free = 0.4398    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4398
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0450
moved from start:          0.7105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8987  Z= 0.176
  Angle     :  0.853  18.314  12219  Z= 0.381
  Chirality :  0.046   0.249   1325
  Planarity :  0.007   0.068   1590
  Dihedral  :  7.648 137.244   1274
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.45 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 27.14 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.25), residues: 1086
  helix:  0.40 (0.26), residues: 396
  sheet: -0.29 (0.41), residues: 171
  loop : -1.19 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 345 
 TYR   0.018   0.002   TYR B 109 
 PHE   0.024   0.003   PHE A 161 
 TRP   0.015   0.001   TRP B 348 
 HIS   0.008   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 8980)
  covalent geometry    : angle       0.79028 (12207)
  hydrogen bonds       : bond        0.03920 (  355)
  hydrogen bonds       : angle       5.38942 ( 1006)
  metal coordination   : bond        0.01193 (    4)
  metal coordination   : angle      10.23749 (   12)
  Misc. bond           : bond        0.02241 (    3)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 41
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  348 LYS cc_start: -0.1853 (OUTLIER) cc_final: -0.2394 (mttt)
REVERT: A  444 ASN cc_start: 0.0885 (OUTLIER) cc_final: -0.1144 (p0)
REVERT: A  486 PHE cc_start: 0.1169 (OUTLIER) cc_final: 0.0862 (m-10)
REVERT: A  539 LEU cc_start: -0.0847 (OUTLIER) cc_final: -0.1176 (mt)
REVERT: B  116 ASN cc_start: 0.2798 (p0) cc_final: 0.1866 (p0)
REVERT: B  136 MET cc_start: 0.2978 (OUTLIER) cc_final: 0.0790 (mmm)
REVERT: B  413 LYS cc_start: 0.2840 (OUTLIER) cc_final: 0.2262 (ptpt)
REVERT: B  432 MET cc_start: 0.5004 (mtm) cc_final: 0.4722 (pmm)
REVERT: B  462 MET cc_start: 0.3158 (OUTLIER) cc_final: -0.0020 (pmm)
REVERT: B  487 MET cc_start: 0.1775 (mpp) cc_final: 0.1209 (mpp)
  outliers start: 38
  outliers final: 22
  residues processed: 69
  average time/residue: 0.4135
  time to fit residues: 31.7427
Evaluate side-chains
  68 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 39
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  533 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 107 optimal weight:    0.3980
   chunk 1 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 91 optimal weight:   40.0000
   chunk 42 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    2.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 HIS
A 564 GLN    A
A 595 GLN
B  26 ASN
** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 397 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5157 r_free = 0.5157 target = 0.313557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.260241 restraints weight = 31191.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.4710 rms_B_bonded: 6.86
r_work: 0.4463 rms_B_bonded: 5.53 restraints_weight: 2.0000
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4465 r_free = 0.4465    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4465 r_free = 0.4465    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.4465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0529
moved from start:          0.8086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107   8987  Z= 0.241
  Angle     :  0.977  15.391  12219  Z= 0.462
  Chirality :  0.050   0.258   1325
  Planarity :  0.008   0.081   1590
  Dihedral  :  8.328 133.366   1274
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 20.52
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.49 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 26.81 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.25), residues: 1086
  helix:  0.12 (0.26), residues: 397
  sheet:  0.03 (0.46), residues: 139
  loop : -1.51 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 373 
 TYR   0.024   0.002   TYR A 101 
 PHE   0.031   0.003   PHE A 168 
 TRP   0.015   0.002   TRP A 540 
 HIS   0.014   0.002   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 8980)
  covalent geometry    : angle       0.92641 (12207)
  hydrogen bonds       : bond        0.04925 (  355)
  hydrogen bonds       : angle       5.94506 ( 1006)
  metal coordination   : bond        0.02773 (    4)
  metal coordination   : angle       9.89699 (   12)
  Misc. bond           : bond        0.06188 (    3)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 39
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.1265 (OUTLIER) cc_final: -0.1096 (p0)
REVERT: A  539 LEU cc_start: -0.0741 (OUTLIER) cc_final: -0.1113 (mt)
REVERT: B   81 LEU cc_start: -0.2026 (OUTLIER) cc_final: -0.2304 (tt)
REVERT: B  136 MET cc_start: 0.3230 (OUTLIER) cc_final: 0.0860 (mmm)
REVERT: B  413 LYS cc_start: 0.2999 (OUTLIER) cc_final: 0.2321 (ptpt)
REVERT: B  462 MET cc_start: 0.3197 (OUTLIER) cc_final: -0.0050 (pmm)
  outliers start: 39
  outliers final: 23
  residues processed: 69
  average time/residue: 0.3661
  time to fit residues: 28.1463
Evaluate side-chains
  64 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 35
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0870
   chunk 90 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:   20.0000
   chunk 102 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.1562

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 430 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5176 r_free = 0.5176 target = 0.316167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.4803 r_free = 0.4803 target = 0.264062 restraints weight = 31325.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.4728 rms_B_bonded: 7.06
r_work: 0.4448 rms_B_bonded: 5.83 restraints_weight: 2.0000
r_work (final): 0.4448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4446
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4446 r_free = 0.4446    target_work(ls_wunit_k1) = 0.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4446 r_free = 0.4446    target_work(ls_wunit_k1) = 0.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.4446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0460
moved from start:          0.8122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8987  Z= 0.159
  Angle     :  0.844  19.277  12219  Z= 0.372
  Chirality :  0.046   0.201   1325
  Planarity :  0.006   0.065   1590
  Dihedral  :  7.752 129.938   1274
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.10 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 28.24 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.25), residues: 1086
  helix:  0.24 (0.26), residues: 404
  sheet: -0.12 (0.46), residues: 140
  loop : -1.31 (0.25), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 113 
 TYR   0.019   0.002   TYR A 527 
 PHE   0.021   0.002   PHE A 168 
 TRP   0.008   0.001   TRP A 197 
 HIS   0.008   0.001   HIS B 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8980)
  covalent geometry    : angle       0.76860 (12207)
  hydrogen bonds       : bond        0.03779 (  355)
  hydrogen bonds       : angle       5.44518 ( 1006)
  metal coordination   : bond        0.01007 (    4)
  metal coordination   : angle      11.14363 (   12)
  Misc. bond           : bond        0.02092 (    3)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 39
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.0771 (OUTLIER) cc_final: -0.1245 (p0)
REVERT: A  532 LEU cc_start: 0.0900 (mp) cc_final: 0.0591 (mt)
REVERT: B   81 LEU cc_start: -0.2150 (OUTLIER) cc_final: -0.2530 (tt)
REVERT: B  117 ARG cc_start: 0.3267 (mtp85) cc_final: 0.0502 (mtp85)
REVERT: B  136 MET cc_start: 0.2793 (OUTLIER) cc_final: 0.0750 (mmm)
REVERT: B  413 LYS cc_start: 0.2824 (OUTLIER) cc_final: 0.2235 (ptpt)
REVERT: B  432 MET cc_start: 0.4773 (mtm) cc_final: 0.4554 (pmm)
REVERT: B  462 MET cc_start: 0.3186 (OUTLIER) cc_final: -0.0104 (pmm)
  outliers start: 30
  outliers final: 22
  residues processed: 61
  average time/residue: 0.3363
  time to fit residues: 23.0527
Evaluate side-chains
  64 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 37
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0770
   chunk 107 optimal weight:    7.9990
   chunk 64 optimal weight:    0.0770
   chunk 61 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.5298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  26 ASN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5185 r_free = 0.5185 target = 0.317257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4915 r_free = 0.4915 target = 0.277361 restraints weight = 29410.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.4871 rms_B_bonded: 4.06
r_work (final): 0.4871
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4877 r_free = 0.4877    target_work(ls_wunit_k1) = 0.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4876 r_free = 0.4876    target_work(ls_wunit_k1) = 0.275         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1002
moved from start:          0.8102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8987  Z= 0.127
  Angle     :  0.762  16.791  12219  Z= 0.329
  Chirality :  0.044   0.220   1325
  Planarity :  0.006   0.067   1590
  Dihedral  :  7.235 131.856   1274
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.64 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 29.12 %
    Favored  : 68.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.25), residues: 1086
  helix:  0.66 (0.26), residues: 403
  sheet: -0.27 (0.42), residues: 172
  loop : -1.08 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 475 
 TYR   0.013   0.001   TYR A 527 
 PHE   0.014   0.001   PHE A 168 
 TRP   0.008   0.001   TRP A 197 
 HIS   0.008   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8980)
  covalent geometry    : angle       0.68834 (12207)
  hydrogen bonds       : bond        0.03216 (  355)
  hydrogen bonds       : angle       4.99539 ( 1006)
  metal coordination   : bond        0.00810 (    4)
  metal coordination   : angle      10.45011 (   12)
  Misc. bond           : bond        0.00965 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2886.99 seconds
wall clock time: 50 minutes 2.01 seconds (3002.01 seconds total)